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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod115

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod115 Module size 17 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 759 CA1 carbonic anhydrase 1 56934 CA10 carbonic anhydrase 10 770 CA11 carbonic anhydrase 11 771 CA12 carbonic anhydrase 12 377677 CA13 carbonic anhydrase 13 23632 CA14 carbonic anhydrase 14 760 CA2 carbonic anhydrase 2 761 CA3 carbonic anhydrase 3 762 CA4 carbonic anhydrase 4 763 CA5A carbonic anhydrase 5A 340591 CA5B carbonic anhydrase 5B pseudogene 1 765 CA6 carbonic anhydrase 6 766 CA7 carbonic anhydrase 7 767 CA8 carbonic anhydrase 8 768 CA9 carbonic anhydrase 9 388695 LYSMD1 LysM domain containing 1 6521 SLC4A1 solute carrier family 4 member 1 (Diego blood group)

Functional annotation

Modules were tested for enrichment in functional and pathway annotations using two complementary approaches:
1. To select a small number of specific / non-redundant annotations for each module, a regression-based approach was used;
2. To obtain the complete set of enriched annotations, an extension of Fisher’s exact test that takes annotation bias into account was employed (Wallenius’ non-central hypergeometric distribution).

Most specific annotations for this module

Coeff.1 P-value.2 Source.3 Term.4 Class.5 5.21e-01 1.01e-49 GO carbonate dehydratase activity molecular_function 2.85e-01 1.33e-39 Reactome Reversible hydration of carbon dioxide Metabolism 7.80e-03 3.51e-11 Reactome Erythrocytes take up oxygen and release carbon dioxide Transport of small molecules 4.63e-03 4.55e-34 GO bicarbonate transport biological_process

¹Regression coefficient

²Fisher’s exact test nominal P-value

³Annotation source (Reactome, GO biological process (BP), molecular function (MF) and cellular component (CC))

⁴GO category or Reactome pathway

⁵High-level branch of annotation tree

Gene membership

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 0.00e+00 0.00e+00 anion transport 0.00e+00 0.00e+00 one-carbon metabolic process 0.00e+00 0.00e+00 bicarbonate transport 0.00e+00 0.00e+00 organic anion transport 0.00e+00 0.00e+00 hydro-lyase activity 0.00e+00 0.00e+00 lyase activity 0.00e+00 0.00e+00 carbonate dehydratase activity 7.49e-07 2.24e-04 basolateral plasma membrane 5.31e-06 2.18e-03 positive regulation of cellular pH reduction 5.91e-06 2.40e-03 regulation of chloride transport 6.55e-06 2.64e-03 positive regulation of synaptic transmission, GABAergic 1.44e-05 3.64e-03 arylesterase activity 2.29e-05 8.09e-03 regulation of intracellular pH 2.30e-05 8.13e-03 regulation of cellular pH 2.81e-05 9.70e-03 regulation of pH 4.28e-05 1.40e-02 regulation of synaptic transmission, GABAergic 1.31e-04 3.67e-02 ion homeostasis 3.93e-04 9.19e-02 positive regulation of synaptic transmission 9.29e-04 1.86e-01 regulation of ion homeostasis 9.41e-04 1.88e-01 cellular cation homeostasis

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 REVERSIBLE HYDRATION OF CARBON DIOXIDE 0.00e+00 0.00e+00 REVERSIBLE HYDRATION OF CARBON DIOXIDE 9.78e-03 7.88e-01 REGULATION OF HYPOXIA INDUCIBLE FACTOR HIF BY OXYGEN

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.28e-05 8.45e-02 increased urine pH 3.35e-05 1.09e-01 stomach epithelial hyperplasia 3.48e-05 1.12e-01 decreased circulating bicarbonate level 9.39e-05 2.17e-01 acidosis 1.10e-03 9.51e-01 abnormal digestive system physiology 1.88e-03 1.00e+00 abnormal mean corpuscular hemoglobin 3.75e-03 1.00e+00 gastric cysts 3.75e-03 1.00e+00 binucleate 3.76e-03 1.00e+00 hyperchromasia 3.76e-03 1.00e+00 stomatocytosis 3.77e-03 1.00e+00 increased blood osmolality 5.61e-03 1.00e+00 hypokalemia 5.62e-03 1.00e+00 abnormal blood pH regulation 5.62e-03 1.00e+00 dilated efferent ductules of testis 5.63e-03 1.00e+00 pyelonephritis 5.64e-03 1.00e+00 acidemia 5.64e-03 1.00e+00 reticulocytopenia 5.64e-03 1.00e+00 absent erythroid progenitor cell 7.48e-03 1.00e+00 renal tubular acidosis 7.49e-03 1.00e+00 abnormal erythroblast morphology

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)